Academic Projects pertaining to Agriculture Biotechnology & OMICs Lab
Ecology & Systematics Plant Stress Physiology Plant genetic diversity
Genomics Bioremidation Plant genetic diversity Tissue Culture OMICs Lab
Chloroplast genomics Mitochondrial genomics Whole genomics Metagenomics
Transcriptomics Bioinformatics Oman Vision-2040
Efficient utilization of Oman’s genetic natural resources will contribute to non-oil share of GDP. Young Omanis development will stand out on top priorities of the envisaged projects.
Scientific research and innovation is a national priority in Oman Vision 2040. Diversification of economical resources to solicit alternatives for oil and gas stands on top of research priorities. NMSRC Strategic Projects
With the Ministry of Agriculture and Fisheries Transcriptomic of Dubas Bug With the Diwan of Royal Court Genomics of Date Palm Trees Office for Conservation of Environment Genomics & Metabolomics of Mango Trees Oman Botanic Garden Genomics & Metabolomics of Bananas
With the Ministry of Health With the Ministry of Higher Education, Molecular Epidemiology and Sequencing of Research and Innovation SARS-CoV-2 Virus Gene Bank of Oman Epidemiology of SARS-CoV-2 infection among High Throughput Screening of Oman health workers Genetic Natural Resources Bacterial Antibiotic Resistance Value addition to our genetic resources
Fragrances Beauty products Documentation Cosmetics Gene bank Skin care Healthcare products Health Products Nutraceuticals Oman Pharmaceuticals Genetic Natural Resources Low calorie sweeteners Nutritional Products Food supplements Flavours Pesticides Establish a solid Ground for Agrochemicals Fertilizers pharmaceutical, cosmeceutical and Growth promoters agrochemical industries Innovation. How simple it can be!
Hook-and-loop fasteners - $100 million a year
George de Mastral produced a prototype and named it velcro, a combination of the works 'velvet' and 'crochet’. . It was patented in 1955. . NASA picked up the brand and began using it for astronaut equipment. . Puma picked up on the brand for kids' shoes. . A worldwide success, bringing in $100 million (£78.6m) revenue every year.
The top down squeeze bottle - $14 million a year
Paul Brown, the owner of a small precision-moulding shop, spent his days coming up with and rethinking the design of the bottle. He said: "I would pretend I was silicone and, if I was injected into a mould, what I would do." His work paid off in 1991, when he came up with the idea for a bottle that would open when squeezed but remain closed if no pressure was applied. . Innovation. How simple it can be!
Fidget spinners - $5 billion a year
Originally invented as a therapeutic tool for kids with ADHD and autism, this simple spinning toy has sold to kids and adults alike since 2017.
Crocs - $1 billion a year
Despite not winning any fashion contests, annual sales of Crocs have regularly exceeded $1 billion (£787m) a year. Launched in the early 2002 by three friends, Crocs were advertised to be made from a trademarked material which was “comfortable, lightweight, non-marking and odor resistant”.
Snap Wraps - $8 million a year
The overwhelming simplicity of Anders' invention pleased kids and pre-teens everywhere. The bracelet worked by simply slapping a straight piece of steel covered in colorful fabric to the wrist, which it instantly clasped itself around. Value addition from our lab. How simple!
Frankincense Animal feeding
Dark date syrup White date syrup
Frankincense crystals Phytohormones-rich oil Use of date palm kernel oil for phytohormones rich One step One step anti-wrinkle cream
Phytohormones-rich oil Animal feeding waste Renewable and One step cost-effective fillers for polymeric materials
Use of palm pollen for treatment of One step skin conditions and anti-aging
Wasted pollen treatment. The use of date palm as a potential Hard carbons issued from date adsorbent for wastewater treatment to palm as efficient anode materials replace activated carbon for sodium-ion batteries Beneficial Outcomes
Paper and Agriculture Biofuels Biosurfactant Health & constructions Beauty Handicrafts Compost Methane Carbon capsules for treatment of stomach gases Wood Fertilizers Hydrogen Healing of wounds and burns Construction Animal feeds- production Making soap- rich of fatty acids materials cows, goats, fish Ethanol Roasted kernels as cacao alternative Paper industry Butanol Date kernels Coffee Date kernels are source of Furfural (30%) used in oil refineries and in pesticides industries Beneficial Outcomes
Biopolymers Organic acids Enzymes Nutraceutical Amino acids
Xanthan gum Citric acid Pectinases Liquid or Tablets Glutamic acid Poly (3- Lactic acid a-Amylase hydroxybutyrate) Curdlan Carotenoid Beneficial Outcomes
Food Biomass Probiotic Date-Palm
Biscuits, pies & pastries production Baker’s yeast lactobacilli Fibers Date chocolate & Tamreya industry Dates Pone, Date jam Wastewater filter Date powder, Date syrup Molasses production (Debs) High-fructose syrup Fructooligosaccharides Beverages industry Ongoing Research Projects pertaining to Agriculture at NMSRC Part 1: Frankincense trees in Oman Boswellia sacra (Frankincense Tree) Boswellia sacra (Chemical Compounds)
Phytochemical Investigation
Frankincense Smoke Project de novo genome sequence of B. sacra 1 We report the de novo genome sequence of B. sacra, comprising 667.8 Mb DNA sequence in genome. Comparison to conserved single copy genes across the eudicot’s species, the data suggests a >97% assembly of the gene space in B. sacra genome.
The combined length of genes was 63.6 Mb or ~9.5% of the whole genome. We found 18,564 high-confidence predictions of protein-encoding genes. The genes found in Boswellia have been found to play a functional role in cell- wall synthesis, arrangement, exfoliating and response to wounds. Additionally, genes related secondary metabolites (flavonoids, phenolics, terpenoids), abiotic stress tolerance, photosynthesis, metabolic and biological processes.
Circular presentation of major scaffolds (brown), gene density (green), location and presence of genes involved in terpenoid biosynthesis (dark blue), simple repeat density (red), transposable elements distribution (blue), LTR-RT density (purple), above/below mean GC% (gray) and inner circle shows the major collinear genes across different scaffolds. Project Genome multiple alignment with taxonomically related species 2
(A) The inner circle shows 19 chromosomes within the grape genome comprising tripled homeologs of seven assumed ancestral chromosomes, and the homoeologous genes are connected by colored lines. The 15 circles can be divided into three groups according to the major eudicot-common hexaploidy (ECH), in which the first group, the inner five circles, represents the orthologs between them, and the other two groups (the intermediate and outer five circles) are paralogs comparing to the first group.
(B) Circles show the multiple alignment between the compared four genomes with Boswellia sacra as reference (B: B. sacra, P: C. papaya, S: C. sinensis, A: A. occidentalie). The five circles show their orthologous relationship between the compared genomes, with A. occidentalie comprising two circles to show an extra genome doubling in its genome, in contrast to the other three genomes. (B) Phylogenetic tree of B. sacra (Bs), A. occidentale (Ao), C. papaya (Cp), C. sinensis(Cs) and V. vinifera (Vv). The core-eudicot common hexaploidy (ECH) is denoted by a blue flash, and the A. occidentale special tetraploidization (AST) is denoted by red flashes.
(C) Gene phylogeny: three paralogous genes in the Evolutionary & comparative Vv, Cp, Bs, Cs and Ao are denoted by Vv1, Vv2, and genomics of B. sacra Vv3, and Cp1, Cp2, and Cp3, and Cs1, Cs2, and Cs3, suggested that the whole and Bs1, Bs2, and BS3, respectively, produced by the genome duplication events ECH, and each has 2 orthologs and 4 out paralogs in occurred 46-52 and 49-55 the Ao genome (e.g., V1 has 2 orthologs, Ao11, million years ago from Ao12, and 4 out paralogs, Ao21, Ao22, Ao31, Ao32 Citrus sinensis (orange) and in Ao genome). The species tree was produced based Anacardium occidentale on the presence of homologous genes. (cashew nut), respectively. (D, E) Ks dating before and after evolutionary rate corrections. Anonymous nucleotide substitution rate (Ks) distribution between the selected genomes. The solid curve lines show the events of polyploidization that appeared in genomes, while the dash lines represent the divergent events between the two compared genomes. The x-axes represent the Ks values and the y-axes represent the density of the compared homologous genes. Boswellia socatrna B. ovalilfoliolata B. frereana B. carterii B elongata B. serrata
B. rivae
B. neglecta B. bullata Different B. dalzielii
species of B. sacra Frankincense trees
B. popviana B. dioscoridis B. ameero Part 2: Date palm trees in Oman Project Date palm genomics 1 Draft Chloroplast Mitochondrial
Region P. dactylifera P. dactylifera P. dactylifera var P. dactylifera vr var Khanezi var Naghal Khalas Aseel LSC Length (bp) 86090 86092 86197 86194 GC(%) 35.3 35.3 35.3 35.3 Length (%) 54.41 54.41 54.39 54.39 SSC Length (bp) 17575 17574 17712 17711 GC(%) 31 31 30.8 30.8 Length (%) 11.10 11.10 11.17 11.17 IR Length (bp) 27273 27272 27277 27276 GC(%) 42.4 42.4 42.4 42.4 Length (%) 17.23 17.23 17.21 17.21 Total GC(%) 37.3 37.3 37.2 37.2 Length (%) 158211 158210 158462 158458 First chloroplast genome dataset for Naghal and Khanizi report Compared at genome and gene levels with Khalas and Aseel Phylogenetic analysis based on the whole genomes and 68 shared genes showed identical phylogenetic trees of Khanezi and Naghal forming clades with Khalas and Aseel cultivars, respectively Gender differentiation in immature date palm leaf with the help of Project Spectroscopic and Molecular methods 2
Robust infrared (near-infrared reflectance spectroscopy (NIRS) and Fourier transform infrared attenuated total reflectance (FTIR/ATR)) and nuclear magnetic resonance (NMR) spectroscopy methods coupled with extensive chemometric analysis were used to identify the sex differentiation in immature date palm leaves
NIRS/FTIR reflectance and 1H-NMR profiling suggested that the signals of monosaccharides (glucose and fructose) and/or disaccharides (maltose and sucrose) play key roles in sex differentiation.
Sex-specific genes and molecular markers obtained from the lower halves of LG12 chromosomes showed enhanced transcript accumulation of mPdIRDP52, mPdIRDP50, and PDK101 in females compared with in males Project Effect of Silicon and Boron and their Interaction on Aluminum uptake and translocation in date palm seedling 3
Si, B and their combination (Si+B) showed a synergistic effect against Al3+ induced chlorosis in date palm seedlings
Si, B or Si+B reduced the level of MDA and O2•- level more significantly under Al3+ stress as compared to the absence of Al3+ stress.
Si, B, and their combination boost Al3+ stress tolerance in date palm seedlings by upregulating the anti-oxidant enzymes, which help date palm seedlings to experienced less oxidative stress, under both normal and Al3+ stress conditions.
Either Si, B or their combination produced less ABA and SA, which indicate that date palm seedlings experienced less stress
Under Al3+ stress conditions, application of either Si, B or Si+B, downregulate ABA biosynthesis genes. Project Transcriptomic analysis of Dubas bug (Ommatissus lybicus Bergevin) infestation to Date Palm 4
We performed RNA-Seq of leaf infected with or without dubas bug to understand the molecular responses of date palm seedlings. Before doing that, we noticed that dubas bug infestation significantly increase superoxide anion and malondialdehyde production to two-folds as compared to healthy control
The infection repercussions were also revealed by significantly higher contents of endogenous phytohormonal signaling of jasmonic acid (JA) and salicylic acid (SA) compared with control
Transcriptome analysis revealed upregulation of 6,919 genes and down-regulation of 2,695 genes in leaf during the infection process
In conclusion, dubas bug infection aggravated defense responses in date palm by gene networks involved in hypersensitive responses (PAR1, RIN4, PBS1 etc.) Project Hypersensitive responses In date palm after dubas bug infection 5 Investigating the integrative effects of silicon (Si) and gibberellic acid (GA3) Project on date palm growth to mitigate heat stress impact: 6 Objectives Phytohormonal modulation Oxidative stress regulation at biochemical and molecular level Regulation of transcript accumulation of Heat shock Proteins (HSP) genes ABA related biosynthetic pathway
Conclusion
Exogenous GA and Si significantly activated the heat shock transcription factors genes, particularly HsfA3, and the anti-oxidative system of date palm by up-regulating the GPX2, Cyt-Cu/Zn SOD, and CAT transcript accumulation. interactive effects of GA and ABA influenced the hormonal cross-talk between SA and ABA by signaling-related genes (PYL4, PYL8, PYR1) and subsequently enhanced date palm growth and development as well as resistance to heat stress. Project Physio-molecular effects of separate and combined cadmium and salinity stress on date palm under silicon applications 7
Conclusion
Application of Si significantly enhanced macronutrient uptake Reduced accumulation of Cd toxicity Alleviated the stress-induced oxidative burst Down regulation of stress-related endogenous hormones (ABA, JA, SA) Differentially modulated stress-responsive genes (GAPDH, Proline transporter 2, cyt Cu/Zn SOD and Abscisic acid receptor PYL4-like). Consequently such physiological and biochemical modulation by Si under combined stresses proved to be effective strategy for enhancing date palm growth and development under metals and salinity contaminated soil Project Si-mediated resistance in date palm to Fusarium oxysporum attack 8 12 PR PTI6 CAT SOD
10
8
6
4
Relativefold change 2
0 control Si Np SI+NP Fungi Si+F NP+F Si+NP+F Treatment
Si treatment significantly enhanced date palm resistance to F. Oxysporum by modulating antioxidant defense system and stress relevant hormonal signaling. Devising Comparative & Complementary Metabolite Annotation Strategies of Unknown Metabolite Annotation on LC-MS/MS Project based Metabolomics Data of Date Palm 9
Introduction Methodology Untargeted metabolomics datasets generated using high Untargeted HR LC MS/MS data was acquired from date palm leaf resolution ( LC MS/MS yields only hundreds of annotations, extracts(n=3) and features were pooled for a unique set of features for this and thousands of unknown features (i.e., defined as a unique study. set of m/z, intensity, and a retention time) of which only a Using an Agilent 6530 LC-Q-ToF platform using a C-18 reverse phase few hundred are identifiable with accurate masses. column on an Agilent 1260 HPLC system run with flow rate of 200µL/min Currently many unknown feature annotation strategies have and data were acquired on positive mode only. evolved and offer a consortia of tools that can aid in Data acquisition parameters were as follows: scan range of 30-1500,scan rate confident identification of metabolites of 2 spectra/sec, and collision energy for MS/MS was10-40eV. Using an example of data palm leaf Methanolic extract, we The data were interrogated using open source tool MS-DIAL for spectral demonstrate the use of two such tools as a strategy for library matching with available open source spectra from MoNA, unknown annotation MassBank,GNPS. Compared two different tools for Unknown Feature annotation (a) MS- FINDER and (b) SIRIUS for compound identification. Results We observed that, out of 238 unknown features, MS-FINDER and SIRIUS aided formulae assignment of 111 and 90 features (belonging to 79 chemical ontologies), respectively, of which 32 were common to both. At the metabolite identification, MS-FINDER and SIRIUS aided annotation of 127 and 53 features, respectively, of which only a single metabolite (isorhoifolin, a 5-o-methylated flavonoid) was common to both strategies.
Isorhoifolin
At the level of annotated metabolites, the single overlap was for Isorhoifolin
Conclusion
Using this comparative analysis, we demonstrated that both the in silico approaches are very complementary in unknown feature annotation, and would benefit from both tools being used for their different algorithms, databases and scoring/ filtering strategies. Part 3: Pomegranates trees in Oman Project Pomegranate genomics 1 Draft Chloroplast Mitochondrial
P. granatum P. L. L. L. L. L. L. L. (Helow) granatum fauriei floribun guilinesi indica interme speciosa subcosta da s dia ta Size (bp) 158630 158633 15244 152240 152193 152205 152330 152476 152049 0 Overall GC contents 36.9 36.9 37.6 37.6 37.6 38.5 37.6 37.6 37.6 LSC size in bp 89015 89017 83923 83967 83817 84046 83987 84051 83890 SSC size in bp 18686 18687 16933 16875 16790 16915 16873 16979 16909 IR size in bp 25466 25465 25792 25699 25793 25622 25736 25723 25625 Protein coding 78159 78816 81327 81045 81333 75204 81300 81309 79644 regions size in bp tRNA size in bp 2816 2790 2809 2742 2741 2787 2810 2742 2824 rRNA size in bp 9050 9050 9050 9044 9044 9050 9050 9046 9042 Number of genes 131 129 130 129 129 134 130 129 129 Number of protein 86 84 85 85 85 86 85 85 84 Comparison of the P. granatum whole cp genome with coding genes seven Lagerstroemia species revealed an overall high Number of rRNA 8 8 8 8 8 8 8 8 8 degree of sequence similarity with divergence among Number of tRNA 37 37 37 36 36 37 37 36 37 intergenic spacers Genes with introns 11 11 11 12 13 12 13 13 13 Part 4: Tomato plant in Oman Project Stress Tolerance and Plant-Microbe Interaction 1
An endophytic fungi isolated from Boswellia sacra’s leaf, showed improved tomato plant Controlled environment growth during heat, drought, salinity and chilling stress
Drought (20% soil moisture) The endophyte application increased the activities of Chilling stress (5C) endogenous phytohormones SA/ABA and showed an Heat stress (40C) increase in gene expression of Salinity stress (140mM) their synthesis
The result proved important to use this strain as plant growth promoting fungi at broader field trails Project Bacteria from medicinal plant and effects on tomato 2 An endophytic bacteria isolated from arid land medicinal plant showed improved tomato plant growth during heat, drought, salinity and chilling stress The whole genome sequence analysis confirmed the presence of genes related to plant growth promotion
DNA extraction
Library Preparation
PacBio Seq
Assembly / annotation
Bioinformatic analysis Project Effect of exogenous application of GABA on uptake of Cd in tomato and increase tolerance level to heavy metal stress by regulating antioxidant enzymes and plant stress responsive hormone 3
Exogenous application of GABA significantly improve tomato plant growth during cd contamination. The cd induced oxidative stress was significantly reduced by GABA application Part 5: Wheat plant in Oman Project Evaluation of Omani wheat landraces against heat and drought stress tolerance through in-depth genomic approaches 1
Stress Tolerant WLR To evaluate the adaptability of selected Omani wheat Cloning and landraces in drought and heat stress conditions and Screening of transformation WLR understand the physio-chemical-molecular expression MP patterns and their responses.
To elucidate and understand the gene(s) responsible for Selecting QTL stress-FIT enhancing drought & heat stress tolerance and identification WLR performing detailed transcriptomic analysis to usher gene networks involved in stress tolerance mechanisms.
To elucidate and characterize selected QTLs through Molecular Bioinformatic SNP, transcriptomic analysis and characterizing the analysis hormone Signaling phenome for tolerant landrace using next-generation sequencing methods Transcriptome Sequencing Experiments In Progress…
Drought Control Drought Control Drought Control Drought Control
Drought Control Drought Control Drought Control Drought Control
Drought Control Drought Control Drought Control Drought Control Part 6: Diversity of different mangoes cultivars in Omani Project Genomic and metabolomics diversity of different Omani mangoes cultivars 1 Introduction
Mango in Oman and is the third largest in production quantity after date palm and banana. The resistance to disease has led to a greater interest in studying the diversity of Omani mangoes to characterize locally grown mango. Limited Information is available on the genetic diversity or germplasm characterization of cultivated mangoes in Oman. Objectives
To assess variability among the Omani mangoes cultivars for different targeted and non-targeted metabolites and fruit quality traits To understand and map-up the metabolomic (primary and secondary) composition of all Omani cultivars of mangoes To establish a strategy to explore the genetic basis controlling metabolite accumulation in Omani mangoes cultivars. To distinguish all cultivars by mapping the essential metabolites for Sugar biosynthesis Characterization of significantly discriminant metabolites contributing to the spatial and phylogenetic chemodiversity. Genomics and Transcriptomics of various cultivars. Genome wide association studies among cultivars.
Results
Hierarchical classification of metabolites Pathway analysis Transcriptomic analysis
Synteny and gene family analysis End of the Presentation